Re: [AMBER-Developers] ifcap and GB - potential problem?

From: Ben Roberts <roberts.qtp.ufl.edu>
Date: Mon, 29 Mar 2010 16:05:35 -0400

OK, I've prepared a patch for rdparm.f that should stop the simulation if ifcap is neither 0 nor 5 and igb or ipb has been enabled. It's attached, and based off the rdparm.f in the release candidate.

Cheers,
Ben

--- rdparm.f.bak 2010-03-29 15:50:16.000000000 -0400
+++ rdparm.f 2010-03-29 16:04:04.000000000 -0400
.@ -537,6 +537,12 @@
       call mexit(6,1)
    end if
    
+ if ((igb /= 0 .or. ipb /= 0) .and. ifcap /= 0 .and. ifcap /= 5) then
+ write(0,*) 'GB/PB calculations are incompatible with spherical solvent caps'
+ write(6,*) 'GB/PB calculations are incompatible with spherical solvent caps'
+ call mexit(6,1)
+ end if
+
    if (( (igb /= 0 .or. ipb /= 0) .and. (ifcap == 0 .or. ifcap == 5)).or.hybridgb>0) then
       fmtin = rfmt
       type = 'RADII'



On 28/3/2010, at 9:27 a.m., Carlos Simmerling wrote:

> I agree too, since hybridgb doesn't use the cap.
>
> On Sat, Mar 27, 2010 at 12:36 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
>
>> Agree ... let's deal with this in Amber12, at least for ipb /= 0 runs.
>>
>> All the best,
>> Ray
>>
>> On Fri, Mar 26, 2010 at 7:21 PM, case <case.biomaps.rutgers.edu> wrote:
>>
>>> On Fri, Mar 26, 2010, Ben Roberts wrote:
>>>>
>>>> ifcap=1, hybridgb>0 = tested to an extent? I tried to read the manual
>>>> here, and
>>>> it didn't really explain the relationship between ifcap (as a setting
>> in
>>> the
>>>> prmtop) and hybridgb. The manual suggests that what hybridgb is really
>>> for, is
>>>> the situation where waters beyond a certain distance away from the
>> solute
>>> (but
>>>> determined by a number of waters to keep) are treated as a continuum.
>> The
>>> example
>>>> (rem_hybrid) does not use ifcap.
>>>
>>> Sorry...my bad. I had assumed that hybridgb used ifcap. Since gb has
>> never
>>> been parameterized with waters, I'd suggest disallowing gb and ifcap
>>> together.
>>> Any other changes should to to Amber12.
>>>
>>> Comments welcome....dac
>>>
>>>
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Received on Mon Mar 29 2010 - 13:30:03 PDT
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